How do you process a supplier invoice that has customs vat on it?

Welcome to the Community, penny9.

If you're trying to create a Bill with different VAT codes or rates per line item. Then, you can do it in your QuickBooks Online (QBO) account. All you have to do is to set the specific VAT on each line item. 

You can refer below articles to learn more how VAT works in QBO:

• How do I set up sales GST/VAT rates and use them on forms? (International QBO)
• VAT Feature Update FAQ
• About your VAT agency

However, if you mean something else, please provide additional information. This is for me to provide the best resolution for you. Take care.